Showing metabocard for 6-Oxopiperidine-2-carboxylic acid (MMDBc0000680)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2020-12-10 18:52:35 UTC
Update Date2024-04-30 19:33:30 UTC
Metabolite IDMMDBc0000680
Metabolite Identification
Common Name6-Oxopiperidine-2-carboxylic acid
Description6-Oxopiperidine-2-carboxylic acid, also known as 6-Oxo-pipecolinic acid, or 6-Oxo-piperidine-2-carboxylic acid, is associated with penicillin V in the production on Penicillium chrysogenum fermentations. Analysis of a 13C NMR spectrum of a concentrated broth from Penicillium chrysogenum fermentation revealed the presence of penicillin V and 6-oxo-piperidine-2-carboxylic acid(1) as the principal constituents. The latter lactam, identical to an authentic sample prepared by the cyclization of alpha-aminoadipic acid was present to the extent of 28 mol% of penicillin V. The lactam isolated form the broth was nearly racemic, having a slight excess of the L-isomer. This isolation provides further evidence regarding the biosynthetic precursors of the hydrophobic penicillins. (PMID: 6788737
Structure
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x00007fdb00718eb8>


  Mrv0541 09041212412D          

 10 10  0  0  0  0            999 V2000
    1.4289   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000    2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  3  1  1  0  0  0  0
  4  2  1  0  0  0  0
  5  3  1  0  0  0  0
  6  4  1  0  0  0  0
  7  4  1  0  0  0  0
  7  5  2  0  0  0  0
  8  5  1  0  0  0  0
  9  6  2  0  0  0  0
 10  6  1  0  0  0  0
M  END
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3D MOL for #<Metabolite:0x00007fdb00718eb8>

HMDB0061705
     RDKit          3D
6-Oxopiperidine-2-carboxylic acid
 19 19  0  0  0  0  0  0  0  0999 V2000
    2.9682   -0.2795   -0.4071 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0326    0.4223    0.0599 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1569    1.0425    1.2786 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8026    0.5313   -0.7866 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3162   -0.8342   -1.1776 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8954   -1.2931   -0.4254 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1296   -0.5444    0.8595 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1342    0.9135    0.5932 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1011    1.7348    1.1653 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2068    1.3450   -0.1810 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.9654    1.5526    1.5974 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1243    1.0691   -1.7051 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1404   -1.5524   -0.9887 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1120   -0.8685   -2.2682 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8722   -2.3725   -0.1654 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8102   -1.1495   -1.0448 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1172   -0.8236    1.2562 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3438   -0.7781    1.6209 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0082    1.8850    0.7188 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  2  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  8 10  2  0
 10  4  1  0
  3 11  1  0
  4 12  1  0
  5 13  1  0
  5 14  1  0
  6 15  1  0
  6 16  1  0
  7 17  1  0
  7 18  1  0
  9 19  1  0
M  END
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3D SDF for #<Metabolite:0x00007fdb00718eb8>


  Mrv0541 09041212412D          

 10 10  0  0  0  0            999 V2000
    1.4289   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000    2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  3  1  1  0  0  0  0
  4  2  1  0  0  0  0
  5  3  1  0  0  0  0
  6  4  1  0  0  0  0
  7  4  1  0  0  0  0
  7  5  2  0  0  0  0
  8  5  1  0  0  0  0
  9  6  2  0  0  0  0
 10  6  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0000680

> <DATABASE_NAME>
MIME

> <SMILES>
OC(=O)C1CCCC(O)=N1

> <INCHI_IDENTIFIER>
InChI=1S/C6H9NO3/c8-5-3-1-2-4(7-5)6(9)10/h4H,1-3H2,(H,7,8)(H,9,10)

> <INCHI_KEY>
FZXCPFJMYOQZCA-UHFFFAOYSA-N

> <FORMULA>
C6H9NO3

> <MOLECULAR_WEIGHT>
143.1406

> <EXACT_MASS>
143.058243159

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_AVERAGE_POLARIZABILITY>
13.591114216564492

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
6-hydroxy-2,3,4,5-tetrahydropyridine-2-carboxylic acid

> <ALOGPS_LOGP>
-0.45

> <JCHEM_LOGP>
0.37450308966666673

> <ALOGPS_LOGS>
-1.10

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
7.452918260085007

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.802293465918679

> <JCHEM_PKA_STRONGEST_BASIC>
1.181689703771606

> <JCHEM_POLAR_SURFACE_AREA>
69.89

> <JCHEM_REFRACTIVITY>
33.2105

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.14e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
6-hydroxy-2,3,4,5-tetrahydropyridine-2-carboxylic acid

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for #<Metabolite:0x00007fdb00718eb8>

HMDB0061705
     RDKit          3D
6-Oxopiperidine-2-carboxylic acid
 19 19  0  0  0  0  0  0  0  0999 V2000
    2.9682   -0.2795   -0.4071 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0326    0.4223    0.0599 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1569    1.0425    1.2786 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8026    0.5313   -0.7866 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3162   -0.8342   -1.1776 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8954   -1.2931   -0.4254 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1296   -0.5444    0.8595 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1342    0.9135    0.5932 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1011    1.7348    1.1653 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2068    1.3450   -0.1810 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.9654    1.5526    1.5974 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1243    1.0691   -1.7051 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1404   -1.5524   -0.9887 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1120   -0.8685   -2.2682 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8722   -2.3725   -0.1654 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8102   -1.1495   -1.0448 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1172   -0.8236    1.2562 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3438   -0.7781    1.6209 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0082    1.8850    0.7188 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  2  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  8 10  2  0
 10  4  1  0
  3 11  1  0
  4 12  1  0
  5 13  1  0
  5 14  1  0
  6 15  1  0
  6 16  1  0
  7 17  1  0
  7 18  1  0
  9 19  1  0
M  END
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PDB for #<Metabolite:0x00007fdb00718eb8>

HEADER    PROTEIN                                 04-SEP-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-SEP-12         0                                  
HETATM    1  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    7  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM    8  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
CONECT    1    2    3                                                       
CONECT    2    1    4                                                       
CONECT    3    1    5                                                       
CONECT    4    2    6    7                                                  
CONECT    5    3    7    8                                                  
CONECT    6    4    9   10                                                  
CONECT    7    4    5                                                       
CONECT    8    5                                                            
CONECT    9    6                                                            
CONECT   10    6                                                            
MASTER        0    0    0    0    0    0    0    0   10    0   20    0
END
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3D PDB for #<Metabolite:0x00007fdb00718eb8>

COMPND    HMDB0061705
HETATM    1  O1  UNL     1       2.968  -0.279  -0.407  1.00  0.00           O  
HETATM    2  C1  UNL     1       2.033   0.422   0.060  1.00  0.00           C  
HETATM    3  O2  UNL     1       2.157   1.043   1.279  1.00  0.00           O  
HETATM    4  C2  UNL     1       0.803   0.531  -0.787  1.00  0.00           C  
HETATM    5  C3  UNL     1       0.316  -0.834  -1.178  1.00  0.00           C  
HETATM    6  C4  UNL     1      -0.895  -1.293  -0.425  1.00  0.00           C  
HETATM    7  C5  UNL     1      -1.130  -0.544   0.859  1.00  0.00           C  
HETATM    8  C6  UNL     1      -1.134   0.913   0.593  1.00  0.00           C  
HETATM    9  O3  UNL     1      -2.101   1.735   1.165  1.00  0.00           O  
HETATM   10  N1  UNL     1      -0.207   1.345  -0.181  1.00  0.00           N  
HETATM   11  H1  UNL     1       2.965   1.553   1.597  1.00  0.00           H  
HETATM   12  H2  UNL     1       1.124   1.069  -1.705  1.00  0.00           H  
HETATM   13  H3  UNL     1       1.140  -1.552  -0.989  1.00  0.00           H  
HETATM   14  H4  UNL     1       0.112  -0.869  -2.268  1.00  0.00           H  
HETATM   15  H5  UNL     1      -0.872  -2.373  -0.165  1.00  0.00           H  
HETATM   16  H6  UNL     1      -1.810  -1.150  -1.045  1.00  0.00           H  
HETATM   17  H7  UNL     1      -2.117  -0.824   1.256  1.00  0.00           H  
HETATM   18  H8  UNL     1      -0.344  -0.778   1.621  1.00  0.00           H  
HETATM   19  H9  UNL     1      -3.008   1.885   0.719  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    4
CONECT    3   11
CONECT    4    5   10   12
CONECT    5    6   13   14
CONECT    6    7   15   16
CONECT    7    8   17   18
CONECT    8    9   10   10
CONECT    9   19
END
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SMILES for #<Metabolite:0x00007fdb00718eb8>

OC(=O)C1CCCC(O)=N1
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INCHI for #<Metabolite:0x00007fdb00718eb8>

InChI=1S/C6H9NO3/c8-5-3-1-2-4(7-5)6(9)10/h4H,1-3H2,(H,7,8)(H,9,10)
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Synonyms
ValueSource
Adipo-2,6-lactamChEBI
Cyclic alpha-aminoadipic acidChEBI
Cyclic a-aminoadipateGenerator
Cyclic a-aminoadipic acidGenerator
Cyclic alpha-aminoadipateGenerator
Cyclic α-aminoadipateGenerator
Cyclic α-aminoadipic acidGenerator
6-Oxopiperidine-2-carboxylateGenerator
6-OPCAHMDB
Molecular FormulaC6H9NO3
Average Mass143.1406
Monoisotopic Mass143.058243159
IUPAC Name6-hydroxy-2,3,4,5-tetrahydropyridine-2-carboxylic acid
Traditional Name6-hydroxy-2,3,4,5-tetrahydropyridine-2-carboxylic acid
CAS Registry NumberNot Available
SMILES
OC(=O)C1CCCC(O)=N1
InChI Identifier
InChI=1S/C6H9NO3/c8-5-3-1-2-4(7-5)6(9)10/h4H,1-3H2,(H,7,8)(H,9,10)
InChI KeyFZXCPFJMYOQZCA-UHFFFAOYSA-N